The optimal surface treatment is an important factor in repairing failed restorations. The aim of this study was to compare the effect of different surface treatments in combination with bonding agents on the repair of an aged nano-filled resin composite. Resin composite disks (N = 180; Filtek Supreme XT, 3M ESPE, St. Paul, MO, USA), 6 mm in diameter and 2 mm in height, were prepared. After accelerated aging of 300 hours in a weathering tester, the specimens were randomly divided into six groups of 30 each, according to the following surface treatment methods: no surface treatment (control group, C), 38% phosphoric acid gel (PA), 9.6% hydrofluoric acid gel (HF), abrasion with sodium bicarbonate particles (SB), aluminum trioxide particle abrasion (AT), and diamond bur (DB). Fresh resin composite was bonded to the treated surfaces with one of two bonding agents (Prime&Bond NT, Dentsply/Caulk, Milford, DE, USA; Clearfil SE Bond, Kuraray Co./J., Morita, Japan). The effect of each surface treatment on the bond strength was determined by a shear bond test. Data were analyzed by two-way analysis of variance and Tukey's post hoc test (p = 0.05). Significant differences were found between the groups, for both surface treatment and bonding agent (p < 0.05). For all surface treatments, the shear bond strengths (SBSs) with Clearfil SE were higher than those with Prime&Bond (p < 0.05). The mean SBS values for the surface treatment groups were, from highest to lowest, 19.3 (DB), 18.7 (AT), 17.4 (SB), 15.2 (HF), 9.2 (C), and 8.8 MPa (PA). Surface treatment with DB or AT was more effective than with the other surface treatments tested for the repair of nano-filled composites. The adhesive used as an intermediate agent is also important in composite repair. Surface treatment with a diamond bur plus a proper adhesive agent is a simple, efficient, and cost-effective procedure for enhancing the shear bond strength of a repaired nano-hybrid resin composite.